Syllabus – Biol 568 Fall 2012 – Disease ecology and evolution Classroom



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Syllabus – Biol 568 Fall 2012 – Disease ecology and evolution


Classroom: Genome Sciences Building, room 1374 (Note this is a CHANGE from Dey Hall 303).

Time: Tuesday / Thursday 11:00am – 12:15pm.
Welcome:

The ecology and evolution of infectious diseases (also known as host-parasite interactions, or host-pathogen interactions) has roots that go back to the early 1900’s. However, it did not begin to emerge as a discipline until around 1980, and has exploded in the current millennium. The class will cover topics such as mathematical theory and models; empirical studies of human, wildlife, insect, and plant host populations; emerging infectious diseases; effects on host behavior; host-parasite coevolution; multi-host systems; multi-pathogen systems; and anthropogenic effects on disease. The greatest depth of understanding has been achieved at the level of population interactions, specifically interactions of a single host population with a single pathogen population. The broader goal of the class is to provide a comprehensive and up-to-date understanding of the causes and consequences of infectious disease at levels from individual organisms to the globe.


Instructor:

Dr. Charles Mitchell

Office hours: Thursday 3:00-4:00PM, and by appointment.

Office: Coker 411

Email: mitchell@bio.unc.edu
Grade:

Letter grades for the class will be based on a curve. The relatively small number of students in the class means that the statistical distribution of raw class scores varies year-to-year. Consequently, the curve of letter grades also varies year-to-year. (In contrast, in Biol 201, the large number of students produces a distribution that is essentially the same every year, which allows us to use the same curve every year.) While I cannot predict this year, in past years in Biol 568, the mean grade has been about a “B”, which is typical for a 500-level Biology class at UNC. Your raw score will be calculated as follows:



  • Transmission exam: 25%

  • Evolution exam: 25%

  • Ecology exam: 25%

  • Final paper: 15%

  • Final oral presentation: 10%


Exams. The exams will include both multiple-choice and open-answer questions. They will seek to elicit higher-level thought processes of analysis, synthesis, and evaluation. With the exception of questions dealing with the mathematical theories covered in the class, doing well on the exams will require going beyond direct recall and simple comprehension.
Class participation. Your active participation in this class will be crucial not only for your own learning, but for that of your classmates. If everyone participates actively, there will be a synergistic benefit for all. Most lectures will include some time for discussion as well. Please come to class prepared with your questions and ideas. To be prepared, please complete the assigned reading(s) in full detail before each lecture.
Final Exam: paper & oral presentation. Instead of a question-based final exam, the final exam will consist of a paper and oral presentation on a topic of each student’s choosing.

  • The topic should either add depth to the class by providing a more advanced exploration of a topic covered in the class, or it should add breadth to the class by covering an additional topic not otherwise covered. (See below for a starter list of possible topics.) To make sure you choose a topic suitable for the class, you need to get instructor approval of your topic. You can get approval by email, during office hour, or after most class meetings. Part of getting approval is to show one reference (i.e. published paper) that you intend to cite. The deadline for getting approval is immediately after the last lecture class.

  • Your paper needs to fit on two pages (single-spaced, with one-inch margins, and 11 point Calibri or similar sized font), including references cited. It needs to cite at least four references that were not class readings. It can also cite readings from class, but these must be a minority of the references cited. All references cited should be in peer-reviewed scientific journals; these appear in the Science Citation Index (http://eresources.lib.unc.edu/eid/list.php?letter=S). Citations in the text, and the list of references cited, should follow the format in the Ostfeld (2008) paper assigned for lecture 17. Avoid plagiarism (http://writingcenter.unc.edu/handouts/plagiarism/). Email your paper to me (as an MS Word file) by NOON on Tuesday 11 December. You also must bring a printed copy to the final exam, and all pages must be stapled (if there is more than one printed page).

  • Each student will give their presentation during the scheduled final exam period. Each presentation should last 5 minutes, which will be followed by 2 minutes for questions. Prepare your presentation in PowerPoint or other program of your choosing. Your file should be no more than 5 MB in size (if it is more, then you need to reduce the resolution of your pictures). Email your file to me (as a PowerPoint or PDF) by 8:00AM the day of the final exam. You also must bring a backup copy to the final exam, either on your laptop or on a USB flash memory drive.

  • You are strongly encouraged to meet with a partner or in small groups to practice and improve your oral presentations. In particular, it is important that your presentation lasts very close to the target of 5 minutes; this takes practice. However, you should not receive any help on your paper; the paper needs to be entirely your own work, following the UNC Honor Code. To avoid violating the honor code, do not discuss your presentation with other people until after you have turned in your paper.


A starter list of some possible paper & oral presentation topics (please don’t limit yourself to these):

Climate change and disease.

Virus evolution.

Disease in social networks

The influence of host social systems.

Heterogeneity in host populations (e.g. “super-spreaders”).

Case studies of pathogen emergence not covered in class.

Real-time monitoring, modeling, and management of epidemics.

Infectious disease through human history (and its future?)
Sakai: Will be used to share readings and communicate announcements.
Please note: Except for the date and time of the final exam, all items in this syllabus are subject to change.
Class schedule
Tue 21 Aug: Lecture 1 – Introduction to disease ecology and evolution.

Reading: none assigned.


Thu 23 Aug: Lecture 2 – (A) Transmission Biology. (B) Microparasite-host dynamics: the basic framework.

Reading 1: Anderson and May 1991, Infectious Diseases of Humans, Ch. 2.

Reading 2: Hastings 1997, Population Biology, Ch. 10.
Tue 28 Aug: Lecture 3 – Microparasite-host dynamics: population models and data.

Reading 1: Anderson and May 1991, Infectious Diseases of Humans, Ch. 2.

Reading 2: Hastings 1997, Population Biology, Ch. 10.
Thu 30 Aug: Lecture 4 – Macroparasite-host dynamics: parasite life-histories and diversity.

Reading: Dobson et al. 1992, Macroparasites: worms and others, chapter in Natural Enemies book edited by Crawley, pages 329-343 only.


Tue 4 Sept: Lecture 5 – Macroparasite-host dynamics: population models and data.

Reading: Dobson et al. 1992, Macroparasites: worms and others, chapter in Natural Enemies book edited by Crawley, pages 329-343 only.


Thu 6 Sept: Lecture 6 – Transmission theory.

Reading 1: McCallum et al. 2001 Trends in Ecology and Evolution, How should transmission be modeled?


Tue 11 Sept: Lecture 7 –Evolution of antibiotic resistance. (Guest lecture by Lisa Bono, UNC Biology)

Reading: Levy 1998, Scientific American, The challenge of antibiotic resistance.


Thu 13 Sept: Lecture 8 – Vector and sexual transmission.

Reading 1: Michalakis and Renaud 2009, Nature, Evolution in vector control.

Reading 2: Anderson and May 1991, Infectious Diseases of Humans, social heterogeneity and STDs: Chap 11.1 and 11.2, except the part from equation (11.2) through (11.7) and all of section 11.2.2 are NOT required.
Tue 18 Sept: Lecture 9 – You are (infected by) what you eat (and drink): environmental transmission.

Reading: Cottingham et al. 2003, Frontiers in Ecology and the Environment, Environmental microbe and human pathogen: the biology and ecology of Vibrio cholerae.


Thu 20 Sept: Lecture 10 – (A) Catch-up. (B) Discussion and review (Q&A format).
Tue 25 Sept: Transmission exam. (covers all material to date, except Lecture 7)
Thu 27 Sept: Lecture 11 – Evolution of virulence.

Reading: Ebert and Herre 1996, Parasitology Today, The evolution of parasitic diseases.


Tue 2 Oct: Lecture 12 – Host-parasite coevolution. Love in the time of cholera: disease and the evolution of sex. The Red Queen hypothesis.

Reading: Lively 1996, BioScience, Host-parasite coevolution and sex (NOTE: The sections on pages 111-113 on "rank order truncation selection" and "the ratchet and the red queen" are NOT required).


Thu 4 Oct: Lecture 13 – Cospeciation.

Reading: Holmes 2010, Nature, The gorilla connection.


Tue 9 Oct: Lecture 14 – Parasites and host behavior.

Reading: Moore 1995, BioScience, The behavior of parasitized animals: when an ant … is not an ant.


Thu 11 Oct: Lecture 15 – Immune dynamics.

Reading 1: Levin and Antia 2001, Science, Why we don’t get sick.

Optional Reading 2: Wobeser (2006) Disease in Wild Animals – Chapter 6 – Defense, resistance, and repair.
Tue 16 Oct: Lecture 16 – Rapid evolution in host-pathogen systems

Reading 1: Earn et al. 2002, Trends in Ecology and Evolution, Ecology and evolution of the flu.

Optional Reading 2: Altizer et al. 2003, Trends in Ecology and Evolution, Rapid evolutionary dynamics and disease threats to biodiversity.
Thu 18 Oct: FALL BREAK.
Tue 23 Oct: Lecture 17 – (A) Pathogen phylodynamics. (B) Discussion and review (Q&A format).

Reading: Grenfell et al. 2004, Science, Unifying the epidemiological and evolutionary dynamics of pathogens.


Thu 25 Oct: Evolution exam. (covers all material to date that was not on the previous exam)
Tue 30 Oct: Lecture 18 – Host population regulation by parasites.

Reading 1: Ostfeld 2008, Journal of Animal Ecology, commentary on Readings 2 and 3.

Optional Reading 2: Pedersen and Greives 2008, Journal of Animal Ecology, The interaction of parasites and resources cause crashes in a wild mouse population.

Optional Reading 3: Hudson et al. 1998, Science, Prevention of population cycles by parasite removal.


Thu 1 Nov: Lecture 19 – Keeping the herd healthy: vaccination, culling, and predation.

Reading: Ostfeld and Holt 2004, Frontiers in Ecology and the Environment, Are predators good for your health?


Tue 6 Nov: Lecture 20 – Disease and conservation biology.

Reading: Cleaveland et al 2007 Conservation Biology, The Conservation Relevance of Epidemiological Research into Carnivore Viral Diseases in the Serengeti.


Thu 8 Nov: Lecture 21 – Parasites in multi-species host communities.

Reading: Keesing et al. 2006, Ecology Letters, Effects of species diversity on disease risk.


Tue 13 Nov: Lecture 22 – When it rains, it pours: hosts with multiple parasites.

Reading: Lafferty 2010 Science, Interacting Parasites.


Thu 15 Nov: Lecture 23 – Emerging parasites I: global patterns.

Reading 1: Woolhouse and Dye 2001 Philosophical Transactions of the Royal Society of London, Preface to Special Issue on Emerging Infectious Diseases.

Reading 2: Daszak et al. 2000 Science, Emerging Infectious Diseases of Wildlife – Threats to Biodiversity and Human Health.
Tue 20 Nov: Lecture 24 – Emerging parasites II: ephemeral outbreaks.

Reading: Lloyd-Smith et al. 2009 Science, Epidemic Dynamics at the Human-Animal Interface.


Thu 22 Nov: THANKSGIVING.
Tue 27 Nov: Lecture 25 – Emerging parasites III: sustained shifts.

Reading: Smith and Guegan 2010 Annual Review of Ecology, Evolution, and Systematics, Changing Geographic Distributions of Human Pathogens.


Thu 29 Nov: Lecture 26 – (A) Parasites as natural enemies: are they really different? (B) Discussion and review (Q&A format).

Reading: Lafferty and Kuris 2002, Trends in Ecology and Evolution, Trophic strategies, animal diversity, and body size.



Last day to get your paper & oral presentation topic approved (by 12:30pm).
Tue 4 Dec: Ecology exam. (covers all material that was not on the previous exams).
Tue 11 Dec: The final version of your final paper is due, via email, by NOON.
Thursday 13 December 12:00-3:00PM in the regular classroom: FINAL EXAM.

  • 8:00AM: The final version if your presentation file is due, via email.

  • 12:00PM: You must hand-in a print-out of your final paper, directly to me.

  • 12:00-3:00PM: Each student will present their final presentation to the class.



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